Generated summary PXD038718 is a DDA label-free dataset (Mus musculus) with 14 runs, 14 samples and enrichment: immunoprecipitation. It was reanalysed with MetaMorpheus 1.1.12. At 1% FDR the search reports 40,677 PSMs, 8,105 peptidoforms and 1,754 protein groups, and the repository holds 2,256 PTM sites for it. 7 open warnings about it are recorded.
Written from catalog fields only (D17), with no model involved. It says nothing the tables below do not.

Open findings

Recorded against this dataset: 0 errors, 7 warnings and 1 for information

cysteine_poor warning
0.33% of 1% target peptides contain C (whole proteomes: 12-26%); check the alkylant (aging PXR-A37)

high_contamination warning
31.63% of protein intensity in the worst file, 10.38% median across 14 files (DEF-QC-9 v3.5)

low_core_use warning
9.99 avg cores of 32 allowed (S5)

low_id_rate warning
The search identified an unusually small fraction of the MS2 spectra. Treat absence of a protein in this dataset as weak evidence. Producer's note: 40677/429323 = 9.47% of MS2 identified (S3)

no_sdrf warning
No SDRF was found for this dataset, so each run was given a synthetic sample of its own. There is no sample metadata: treat every sample as unannotated.

occupancy_not_stored warning
Of 2782 occupancy entries MetaMorpheus wrote, some are not in ptm_stoichiometry: 986 site not in ptm_sites. 'site not in ptm_sites' means the entry's site has no ptm_sites row to key on; 'not determinable' means a cell's segments could not be assigned to its accessions from the sequences (QuantProject DEF-OCC-ACCESSION), which is never guessed. Absence of a row for these sites is therefore not NA. A 'duplicate' is a second entry for a (site, run) that already has a row: one with identical values loses nothing; one with DIFFERENT values means MetaMorpheus wrote two answers and the first in file order was stored (examples in bundle.json occupancy.differing_duplicates; which one should be stored is QuantProject's to define).

unplaced_ptm_sites warning
Some modifications on peptides shared between proteins were not written to ptm_sites for one or more of those proteins, because the peptide could not be located in that protein's sequence and the producer's residue spans cannot be paired with its accessions. Of the (PSM, protein) pairs affected: 48 named a protein that does not contain the stored peptide -- typically a PSM ambiguous between peptide sequences (level 4 or 5), where this protein carries a different candidate than the first, which is the one stored. Sites on the other proteins of the same PSMs are written. Counts are in bundle.json under protein_databases.

occupancy_decoy_groups info
12 occupancy entries on decoy protein groups were not stored: MetaMorpheus computes them, and they are FDR machinery, not biology.

What was found

PSMs at 1% FDR	40,677
Peptidoforms at 1% FDR	8,105
Protein groups at 1% FDR	1,754
PTM sites	2,256
Quantitative values	78,466
PSMs, all (including decoys and sub-threshold)	1,127,681
MS2 identification rate (pxreprise:DEF-ID-RATE)	9.5%
Contaminant share of PSMs (pxreprise:DEF-CONTAM-PSM)	6.0%

How it was measured

Organism searched: Mus musculus (the protein database's organism, not a statement about the samples)
Acquisition: DDA
Quantification: label_free
Labelling: none
Enrichment: immunoprecipitation
Instrument vendor: not recorded
Runs / samples: 14 / 14
Sample metadata: absent
Search engine: MetaMorpheus 1.1.12
Protein database: UP000000589_all_genecentric_2026_03_agingPTM-v3.xml
Pipeline commit: ef0213be9f73

Modifications

Search engine's name	UNIMOD	Sites
Oxidation on M	UNIMOD:35	1,401
Phosphoserine on S	UNIMOD:21	202
Carbamidomethyl on C	UNIMOD:4	177
N-acetylalanine on A	UNIMOD:1	77
Hydroxylation on P	UNIMOD:35	45
Phosphothreonine on T	UNIMOD:21	30
N-acetylserine on S	UNIMOD:1	27
Acetylation on X	UNIMOD:1	23
N-acetylmethionine on M	UNIMOD:1	21
4-hydroxyproline on P	UNIMOD:35	17
GG (Ubiquitination Site) on K	UNIMOD:121	15
N6-glutaryllysine on K	—	15
N6-methacryllysine on K	—	15
N6-acetyllysine on K	UNIMOD:1	13
Phosphorylation on S	UNIMOD:21	13
Asymmetric dimethylarginine on R	UNIMOD:36	9
N6,N6-dimethyllysine on K	UNIMOD:36	9
Hydroxylation on K	UNIMOD:35	8
N-acetylthreonine on T	UNIMOD:1	7
Phosphorylation on T	UNIMOD:21	7
Deamidated asparagine on N	UNIMOD:7	6
Methylation on K	UNIMOD:34	6
HexNAc on S	UNIMOD:43	5
Omega-N-methylarginine on R	UNIMOD:34	5
N-acetylglycine on G	UNIMOD:1	3
N6-crotonyllysine on K	—	3
Phosphotyrosine on Y	UNIMOD:21	3
Tele-methylhistidine on H	UNIMOD:34	3
3-hydroxyproline on P	UNIMOD:35	2
5-glutamyl glycerylphosphorylethanolamine on E	UNIMOD:396	2
Dimethylated arginine on R	UNIMOD:36	2
Glutarylation on K	UNIMOD:1848	2
HexNAc on T	UNIMOD:43	2
Methylation on R	UNIMOD:34	2
N-acetylvaline on V	UNIMOD:1	2
N6-methyllysine on K	UNIMOD:34	2
5-hydroxylysine on K	UNIMOD:35	1
Acetylation on K	UNIMOD:1	1
Citrulline on R	UNIMOD:7	1
Deamidated glutamine on Q	UNIMOD:7	1
Dimethylation on K	UNIMOD:36	1
Dimethylation on R	UNIMOD:36	1
Hydroxyproline on P	UNIMOD:35	1
N6,N6,N6-trimethyllysine on K	UNIMOD:37	1
N6-(pyridoxal phosphate)lysine on K	UNIMOD:46	1
N6-succinyllysine on K	—	1
Phosphorylation on Y	UNIMOD:21	1
Trimethylation on K	UNIMOD:37	1

Every modification with a site on a target protein, most frequent first. A dash in the UNIMOD column means the modification has no UNIMOD term in the registry that searched it, not that it is unknown. One chemistry can appear under two names (UniProt's and MetaMorpheus's); the catalog's ptm_sites_by_chemistry view merges them.

Data

The Parquet files for this dataset are not published yet.

Bundle: 63e69eafcd1b5f3e, written 2026-10-29T13:26:21+00:00 by ingester 1.4.0
Reconciliation: every check agreed with the producer's own counts
Licence: CC-BY-4.0
Credit: NCEMS Aging Proteome Working Group